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PMC:7558333 / 4515-8506 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T10 440-446 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T11 700-706 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T12 717-721 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T13 936-941 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T14 952-957 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T15 977-982 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T16 1110-1115 Body_part denotes Organ http://purl.org/sig/ont/fma/fma67498
T17 2485-2488 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T18 2815-2820 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T19 2957-2965 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T20 2985-2988 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T21 3096-3101 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T22 3281-3284 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 440-446 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T8 700-706 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T9 936-941 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T10 952-957 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T11 977-982 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T12 1110-1115 Body_part denotes Organ http://purl.obolibrary.org/obo/UBERON_0000062
T13 2815-2820 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T14 3096-3101 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T36 131-139 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T37 373-381 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 629-637 Disease denotes diabetes http://purl.obolibrary.org/obo/MONDO_0005015
T39 639-675 Disease denotes hypertension, cardiovascular disease http://purl.obolibrary.org/obo/MONDO_0001302
T40 639-651 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T41 653-675 Disease denotes cardiovascular disease http://purl.obolibrary.org/obo/MONDO_0004995
T42 677-694 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T43 700-714 Disease denotes kidney disease http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240
T45 2361-2369 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T29 128-129 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 221-222 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 700-706 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T32 700-706 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T33 700-706 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T34 925-926 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 936-941 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T36 936-941 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T37 970-975 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T38 977-982 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T39 1110-1115 http://purl.obolibrary.org/obo/UBERON_0003103 denotes Organ
T40 2518-2523 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T41 2540-2541 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 2558-2564 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T43 2598-2599 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T44 2626-2627 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 2791-2796 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T46 3194-3195 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 3210-3216 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T48 3299-3300 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 3488-3492 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T50 3512-3517 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T51 3621-3625 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T52 3627-3632 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T53 3747-3752 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T54 3885-3893 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 639-651 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T3 653-675 Phenotype denotes cardiovascular disease http://purl.obolibrary.org/obo/HP_0001626
T4 700-714 Phenotype denotes kidney disease http://purl.obolibrary.org/obo/HP_0000112
T5 1095-1101 Phenotype denotes Sepsis http://purl.obolibrary.org/obo/HP_0100806

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 474-495 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T3 482-495 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T4 2422-2427 http://purl.obolibrary.org/obo/GO_0019835 denotes Lysis

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T8 1481-1483 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T9 2841-2843 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T10 2854-2856 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T34 0-2 Sentence denotes 2.
T35 3-24 Sentence denotes Materials and Methods
T36 26-30 Sentence denotes 2.1.
T37 31-53 Sentence denotes Population of Patients
T38 54-267 Sentence denotes Forty-five intubated and mechanically ventilated patients hospitalized in a “COVID-19 ICU” of Rennes teaching hospital were screened for this study and benefited from a systematic monitoring to detect Aspergillus.
T39 268-356 Sentence denotes The hospital’s ethics committee (N 20-56 obtained the 30 April 2020) approved the study.
T40 357-539 Sentence denotes The presence of SARS-CoV-2 in respiratory specimens (nasal and pharyngeal swabs or sputum) was detected by real time reverse transcription-polymerase chain reaction (RT-PCR) methods.
T41 540-880 Sentence denotes The following data were recorded: age, patient’s preexisting condition (current smoking, diabetes, hypertension, cardiovascular disease, pulmonary disease, and kidney disease), body mass index, ICU length of stay, duration of mechanical ventilation, ventilator-free days at day 28, need for prone position ventilation, and death in the ICU.
T42 881-976 Sentence denotes Initial clinical laboratory workup included a complete blood count and serum biochemical tests.
T43 977-1038 Sentence denotes Chest CT scans were performed during the ICU hospitalization.
T44 1039-1241 Sentence denotes The Simplified Acute Physiology Score (SAPS II) and the Sepsis-Related Organ Failure Assessment (SOFA) score at admission in ICU, at day 7 and 14 days after admission were used to assess severity [7,8].
T45 1243-1247 Sentence denotes 2.2.
T46 1248-1269 Sentence denotes Aspergillus Detection
T47 1270-1541 Sentence denotes Respiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.
T48 1542-1646 Sentence denotes Briefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking.
T49 1647-1859 Sentence denotes Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C.
T50 1860-2105 Sentence denotes Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9].
T51 2106-2269 Sentence denotes Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).
T52 2270-2574 Sentence denotes For molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen).
T53 2575-2695 Sentence denotes Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].
T54 2696-3045 Sentence denotes In case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis.
T55 3046-3280 Sentence denotes Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations.
T56 3281-3317 Sentence denotes DNA was eluted in a volume of 50 µL.
T57 3319-3323 Sentence denotes 2.3.
T58 3324-3344 Sentence denotes Statistical Analysis
T59 3345-3493 Sentence denotes Continuous variables were expressed as median (interquartile range, IQR) and compared using the nonparametric Mann–Whitney U or Kruskal–Wallis test.
T60 3494-3572 Sentence denotes Dunn’s correction tests were performed if multiple comparisons were requested.
T61 3573-3626 Sentence denotes Qualitative data were compared using Chi-square test.
T62 3627-3690 Sentence denotes Tests were two-sided with significance set at α less than 0.05.
T63 3691-3841 Sentence denotes Concordance between categorical results from diagnostic tests was performed using the percent agreement coefficient and Cohen’s kappa coefficient (κ).
T64 3842-3904 Sentence denotes When comparing quantitative data, an ANOVA test was performed.
T65 3905-3991 Sentence denotes All data were analyzed with GraphPad Prism 8.4 (GraphPad Software, La Jolla, CA, USA).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
121 103-111 Species denotes patients Tax:9606
122 255-266 Species denotes Aspergillus Tax:746128
123 131-139 Disease denotes COVID-19 MESH:C000657245
125 373-383 Species denotes SARS-CoV-2 Tax:2697049
134 579-586 Species denotes patient Tax:9606
135 629-637 Disease denotes diabetes MESH:D003920
136 639-651 Disease denotes hypertension MESH:D006973
137 653-675 Disease denotes cardiovascular disease MESH:D002318
138 677-694 Disease denotes pulmonary disease MESH:D008171
139 700-714 Disease denotes kidney disease MESH:D007674
140 863-868 Disease denotes death MESH:D003643
141 1095-1123 Disease denotes Sepsis-Related Organ Failure MESH:D009102
143 1248-1259 Species denotes Aspergillus Tax:746128
146 1395-1406 Species denotes Aspergillus Tax:746128
147 1481-1483 Chemical denotes GM MESH:C012990
149 1767-1806 Chemical denotes Sabouraud-Chloramphenicol dextrose Agar
154 2361-2371 Species denotes SARS-CoV-2 Tax:2697049
155 2598-2610 Species denotes A. fumigatus Tax:746128
156 2637-2648 Species denotes Aspergillus Tax:746128
157 2418-2427 Disease denotes ATL Lysis MESH:D015275
165 2707-2718 Species denotes Aspergillus Tax:746128
166 2907-2918 Species denotes Aspergillus Tax:746128
167 2945-2956 Species denotes Aspergillus Tax:746128
168 3055-3066 Species denotes Aspergillus Tax:746128
169 2841-2843 Chemical denotes GM MESH:C012990
170 2845-2868 Disease denotes Platelia GM Aspergillus MESH:C562602
171 2976-3000 Disease denotes Platelia IgG Aspergillus MESH:D017099

2_test

Id Subject Object Predicate Lexical cue
32664423-8254858-60101695 1236-1237 8254858 denotes 7
32664423-31775846-60101696 1238-1239 31775846 denotes 8
32664423-28637907-60101697 2264-2266 28637907 denotes 10
32664423-29248586-60101698 2688-2690 29248586 denotes 11
32664423-14766869-60101699 2691-2693 14766869 denotes 12